ScanOrchestrator.java

// SPDX-License-Identifier: Apache-2.0

// Copyright 2026 Egothor

// Copyright 2026 Accenture

package org.egothor.methodatlas.command;

import java.io.IOException;

import java.nio.file.Path;

import java.util.ArrayList;

import java.util.LinkedHashMap;

import java.util.List;

import java.util.Map;

import java.util.Optional;

import java.util.logging.Level;

import java.util.logging.Logger;

import java.util.stream.Collectors;

import org.egothor.methodatlas.AiCacheEntry;

import org.egothor.methodatlas.AiCacheStore;

import org.egothor.methodatlas.AiResultCache;

import org.egothor.methodatlas.emit.ClassificationOverride;

import org.egothor.methodatlas.CliConfig;

import org.egothor.methodatlas.emit.CompositeTestMethodSink;

import org.egothor.methodatlas.emit.TestMethodSink;

import org.egothor.methodatlas.ai.AiClassSuggestion;

import org.egothor.methodatlas.ai.AiMethodSuggestion;

import org.egothor.methodatlas.ai.AiOptions;

import org.egothor.methodatlas.ai.AiSuggestionEngine;

import org.egothor.methodatlas.ai.AiSuggestionException;

import org.egothor.methodatlas.ai.CredentialTriageVerdict;

import org.egothor.methodatlas.ai.PromptBuilder;

import org.egothor.methodatlas.ai.SuggestionLookup;

import org.egothor.methodatlas.api.DiscoveredMethod;

import org.egothor.methodatlas.api.TestDiscovery;

import org.egothor.methodatlas.api.TestDiscoveryConfig;

/**

 * Orchestrates the scan-and-emit loop that every command mode is built around.

 *

 * <p>

 * Each {@link Command} mode varies in three places — output format, per-record

 * sink behaviour, and whether records stream or buffer — but they all share

 * the same core sequence:

 * </p>

 * <ol>

 *   <li>Load all configured {@link TestDiscovery} providers.</li>

 *   <li>For each scan root, run every provider, merge their results, and

 *       group methods by class.</li>

 *   <li>For each class, optionally consult the AI engine through a layered

 *       cache + override lookup.</li>

 *   <li>Forward each method record to the supplied sink.</li>

 *   <li>Close all providers.</li>

 * </ol>

 *

 * <p>

 * This class owns that sequence. Commands compose it with a

 * {@link PluginLoader} (passed in at construction) and configure the

 * per-record sink, AI runtime, and content-hash policy at call time.

 * </p>

 *

 * <h2>API shape</h2>

 *

 * <p>

 * Two entry points serve the two common patterns:

 * </p>

 * <ul>

 *   <li>{@link #scan} manages the provider lifecycle internally; it is the

 *       right call for SARIF, JSON, and GitHub-annotation modes that buffer

 *       or emit unconditionally.</li>

 *   <li>{@link #runDiscovery} processes a single root against pre-loaded

 *       providers; it is the right call for CSV and plain-text modes that

 *       compute per-root metadata (such as the {@code source_root} column)

 *       before forwarding records.</li>

 * </ul>

 *

 * <p>

 * The apply-tags flow has its own shape: {@link #collectMethodsByFile}

 * groups discovered methods by source file (the caller owns the provider

 * lifecycle so it can read each provider's

 * {@link TestDiscovery#hadErrors()} afterwards), and

 * {@link #gatherAiSuggestionsForFile} resolves AI suggestions for one

 * file at a time.

 * </p>

 *

 * <h2>Thread safety</h2>

 *

 * <p>

 * This class is thread-safe. The injected {@link PluginLoader} is

 * thread-safe and {@link java.util.ServiceLoader} resolution is

 * idempotent; nothing else is shared between calls.

 * </p>

 *

 * @see PluginLoader

 * @see AiRuntime

 * @see Command

 * @since 1.0.0

 */

public final class ScanOrchestrator {

    private final PluginLoader pluginLoader;

    /**

     * Optional secondary sink that observes every record alongside the

     * command's primary sink. {@code null} means no fan-out.

     */

    private final TestMethodSink extraSink;

    /**

     * Creates a new orchestrator with no extra sink.

     *

     * @param pluginLoader plugin loader used by {@link #scan} and

     *                     {@link #collectMethodsByFile}; must not be

     *                     {@code null}

     */

    public ScanOrchestrator(PluginLoader pluginLoader) {

    /**

     * Creates a new orchestrator that fans out every record to {@code extraSink}

     * in addition to the command's primary sink.

     *

     * <p>

     * The extra sink, when present, is composed with the primary sink at the

     * {@link #runDiscovery} boundary so every command mode (SARIF, JSON, CSV,

     * GitHub annotations) sees the same fan-out automatically. When

     * {@code extraSink} is {@link Optional#empty()} the orchestrator behaves

     * identically to the legacy single-sink constructor.

     * </p>

     *

     * @param pluginLoader plugin loader used by {@link #scan} and

     *                     {@link #collectMethodsByFile}; must not be

     *                     {@code null}

     * @param extraSink    optional secondary sink invoked in addition to the

     *                     command-supplied primary sink; must not be

     *                     {@code null} (use {@link Optional#empty()})

     */

    /**

     * Scans every configured root, forwarding each discovered test method to

     * {@code sink}. Loads and closes the {@link TestDiscovery} providers

     * internally so callers do not need to manage the lifecycle.

     *

     * <p>

     * When {@code secretCtx} is supplied, credential triage is folded into each

     * per-class AI call so the class source is sent to the provider once for both

     * classification and triage; pass {@code null} for classification only.

     * </p>

     *

     * @param roots           source roots to scan; must not be {@code null}

     * @param cliConfig       full parsed CLI configuration

     * @param discoveryConfig discovery configuration forwarded to providers

     * @param aiEngine        AI engine providing suggestions; may be

     *                        {@code null} when AI is disabled

     * @param sink            receiver of discovered test method records

     * @param override        human classification overrides

     * @param aiCache         AI result cache

     * @param secretCtx       credential-triage context, or {@code null} to disable

     *                        the fold (classification only)

     * @return {@code 0} if all files were processed successfully, {@code 1}

     *         if any file produced a parse or processing error

     * @throws IOException if traversing a file tree fails

     * @since 1.0.0

     */

    public int scan(List<Path> roots, CliConfig cliConfig, TestDiscoveryConfig discoveryConfig,

            AiSuggestionEngine aiEngine, TestMethodSink sink,

            ClassificationOverride override, AiResultCache aiCache,

            CredentialTriageContext secretCtx) throws IOException {

        // Accumulates one cache entry per processed class across all roots; written

        // once at the end when -ai-cache-out is set.

        Map<String, AiCacheEntry> cacheAll =

        try {

                }

                }

        } finally {

        }

    }

    /**

     * Runs all configured {@link TestDiscovery} providers on {@code root},

     * merges their results, orchestrates AI analysis per class, and forwards

     * each method record to {@code sink}.

     *

     * <p>

     * Providers are passed in pre-loaded; callers manage the lifecycle

     * (typically through {@link PluginLoader#closeAll(List)} in a

     * {@code finally} block) so that they can share one provider list across

     * multiple roots while still computing per-root metadata before each

     * call.

     * </p>

     *

     * <p>

     * When {@code secretCtx} is supplied, credential triage is folded into each

     * per-class AI call; pass {@code null} for classification only.

     * </p>

     *

     * @param root               directory to scan

     * @param providers          list of pre-configured discovery providers

     * @param aiOptions          AI configuration for the current run

     * @param aiEngine           AI engine, or {@code null} when AI is disabled

     * @param sink               receiver of discovered test method records

     * @param contentHashEnabled whether to include the class content hash in

     *                           emitted records

     * @param override           human classification overrides

     * @param aiCache            AI result cache

     * @param secretCtx          credential-triage context, or {@code null} to disable the fold

     * @return {@code true} if any provider encountered a parse or processing

     *         error

     * @throws IOException if traversing the file tree fails

     * @since 1.0.0

     */

    public boolean runDiscovery(Path root, List<TestDiscovery> providers,

            AiOptions aiOptions, AiSuggestionEngine aiEngine, TestMethodSink sink,

            boolean contentHashEnabled, ClassificationOverride override,

            AiResultCache aiCache, CredentialTriageContext secretCtx) throws IOException {

    }

    /**

     * Body of {@link #runDiscovery(Path, List, AiOptions, AiSuggestionEngine, TestMethodSink,

     * boolean, ClassificationOverride, AiResultCache, CredentialTriageContext)} that also returns one

     * {@link AiCacheEntry} per processed class (cache hits preserved, misses freshly computed) so the

     * caller can persist the unified AI result cache.

     *

     * @return the error flag plus the per-class cache entries keyed by content hash

     */

    @SuppressWarnings("PMD.CloseResource") // providers are owned by the caller; this method does not close them

    private DiscoveryResult runDiscoveryInternal(Path root, List<TestDiscovery> providers,

            AiOptions aiOptions, AiSuggestionEngine aiEngine, TestMethodSink sink,

            boolean contentHashEnabled, ClassificationOverride override,

            AiResultCache aiCache, CredentialTriageContext secretCtx) throws IOException {

            }

        // The prompt-catalogue signature gates cache reuse and tags written entries;

        // only meaningful when AI is enabled.

                    effectiveSink, cacheEntries);

    }

    /**

     * Classifies one class (consulting the cache), feeds its methods to {@code effectiveSink}, and —

     * when AI produced a cacheable answer with a content hash — records a cache entry.

     *

     * @param entry           one class's discovered methods, keyed by FQCN

     * @param ai              AI runtime (engine, override, cache)

     * @param promptSignature current prompt-catalogue signature, or {@code null} when AI is disabled

     * @param contentHashEnabled whether the emitted records carry the content hash

     * @param secretCtx       credential-triage context, or {@code null}

     * @param effectiveSink   sink receiving the per-method records

     * @param cacheEntries    accumulator to record the cacheable answer into, keyed by content hash

     * @throws IOException if the sink fails to record a method

     */

    private void processClass(Map.Entry<String, List<DiscoveredMethod>> entry, AiRuntime ai,

            String promptSignature, boolean contentHashEnabled, CredentialTriageContext secretCtx,

            TestMethodSink effectiveSink, Map<String, AiCacheEntry> cacheEntries) throws IOException {

        // groupingBy never produces an empty value list, so the first method is always

        // present; it is the representative carrying the class-level fields (source

        // content and file stem are identical across a class's methods).

        // The content hash is needed to read the cache, to emit the hash column, and to

        // key a written cache entry — so compute it whenever any of those apply.

                targetMethods, ai, lookupHash, promptSignature, secretCtx);

        }

    /**

     * Wraps {@code primary} with {@link CompositeTestMethodSink} when an

     * extra sink was supplied to the constructor; returns {@code primary}

     * unchanged otherwise.

     *

     * @param primary command-supplied primary sink

     * @return effective sink to feed during this discovery pass

     */

    private TestMethodSink wrapWithExtraSink(TestMethodSink primary) {

        }

    }

    /**

     * Collects all discovered methods from every configured root, keyed by

     * source-file path. Methods whose {@link DiscoveredMethod#filePath()} is

     * {@code null} are silently skipped.

     *

     * <p>

     * Providers are passed in pre-loaded so the caller can read each

     * provider's {@link TestDiscovery#hadErrors()} after the call and decide

     * how to propagate the exit code; the caller also owns closing them.

     * </p>

     *

     * @param roots     scan roots; must not be {@code null}

     * @param providers configured and already-loaded discovery providers;

     *                  must not be {@code null}

     * @return mutable map from source-file path to the methods found in that

     *         file; insertion order matches discovery order

     * @throws IOException if directory traversal fails for any root

     */

    @SuppressWarnings({"PMD.AvoidInstantiatingObjectsInLoops",

            "PMD.CloseResource"}) // providers are owned by the caller

    public Map<Path, List<DiscoveredMethod>> collectMethodsByFile(

            List<Path> roots, List<TestDiscovery> providers) throws IOException {

                    }

    }

    /**

     * Resolves AI security-classification suggestions for every class in

     * {@code byClass} and populates {@code tagsToApply} and

     * {@code displayNames} with the results for methods that are

     * security-relevant.

     *

     * <p>

     * A display-name suggestion is only placed into {@code displayNames}

     * when the discovered method has no existing {@code @DisplayName} in

     * source (i.e. {@link DiscoveredMethod#displayName()} returns

     * {@code null}). This prevents AI-generated names from overwriting

     * manually authored ones.

     * </p>

     *

     * @param byClass      discovered methods grouped by FQCN for one source file

     * @param ai           AI runtime carrying the engine, override, and cache

     * @param aiCache      AI result cache used to compute the content-hash lookup key

     * @param tagsToApply  output accumulator: method name to tag values to write

     * @param displayNames output accumulator: method name to display name to write

     * @since 1.0.0

     */

    public void gatherAiSuggestionsForFile(Map<String, List<DiscoveredMethod>> byClass,

            AiRuntime ai, AiResultCache aiCache,

            Map<String, List<String>> tagsToApply, Map<String, String> displayNames) {

            // groupingBy never produces an empty value list; the first method is the

            // representative carrying the class-level fields (source content and file

            // stem are identical across a class's methods).

                    fileStem, fqcn, classSource, methodNames, targetMethods, ai, lookupHash,

                }

                }

                }

    /**

     * Wraps a {@link TestMethodSink} so that only records that pass all

     * active filters are forwarded to {@code delegate}.

     *

     * <p>

     * Two independent filters are supported and composed in order:

     * </p>

     * <ol>

     *   <li><b>Security-only filter</b> — when {@code securityOnly} is

     *       {@code true}, records whose {@link AiMethodSuggestion} is

     *       {@code null} or has {@code securityRelevant=false} are dropped.</li>

     *   <li><b>Confidence threshold filter</b> — when {@code confidenceEnabled}

     *       is {@code true} <em>and</em> {@code minConfidence > 0.0}, records

     *       whose {@link AiMethodSuggestion} is {@code null} or has a

     *       {@link AiMethodSuggestion#confidence()} below {@code minConfidence}

     *       are dropped. This filter is a no-op when {@code confidenceEnabled}

     *       is {@code false} because the confidence field is always

     *       {@code 0.0} when confidence scoring was not requested.</li>

     * </ol>

     *

     * <p>

     * When neither filter is active the original {@code delegate} is

     * returned unchanged (zero overhead).

     * </p>

     *

     * @param delegate          the underlying sink to forward matching

     *                          records to

     * @param securityOnly      whether to enable the security-relevance filter

     * @param minConfidence     minimum confidence score (inclusive) required

     *                          to pass the confidence filter; {@code 0.0}

     *                          disables it

     * @param confidenceEnabled whether confidence scoring was requested;

     *                          must be {@code true} for the confidence

     *                          filter to activate

     * @return filtered sink, or {@code delegate} unchanged when all filters

     *         are off

     * @since 1.0.0

     */

    public TestMethodSink filterSink(TestMethodSink delegate, boolean securityOnly,

            double minConfidence, boolean confidenceEnabled) {

                }

        }

                }

        }

    }

    // -------------------------------------------------------------------------

    // Static utilities

    // -------------------------------------------------------------------------

    /**

     * Converts a single discovered test method into a prompt target descriptor.

     *

     * <p>

     * Exposed publicly because {@link ManualPrepareCommand} also needs to

     * build prompt-target lists from discovered methods when writing manual

     * work files; the conversion logic must stay aligned across both call

     * sites to keep the prompt format consistent.

     * </p>

     *

     * @param m discovered test method; must not be {@code null}

     * @return corresponding prompt target descriptor; never {@code null}

     * @see PromptBuilder.TargetMethod

     */

    public static PromptBuilder.TargetMethod toTargetMethod(DiscoveredMethod m) {

    }

    // -------------------------------------------------------------------------

    // Private helpers

    // -------------------------------------------------------------------------

    /**

     * Resolves the AI answer for one class, consulting the signature-gated cache

     * before any provider call and serving cached credential verdicts when present.

     *

     * @param promptSignature the current run's prompt-catalogue signature, or

     *                        {@code null} when AI is disabled

     * @return the override-applied lookup plus the raw answer to cache (or

     *         {@code null} when nothing should be cached)

     */

    private static Resolved resolveSuggestionLookup(String fileStem, String fqcn,

            String classSource, List<String> methodNames, List<PromptBuilder.TargetMethod> targetMethods,

            AiRuntime ai, String contentHash, String promptSignature, CredentialTriageContext secretCtx) {

        }

        }

        List<PromptBuilder.CredentialCandidateRef> candidates =

        // Cache first, gated on the prompt-catalogue signature. A hit serves the

        // classification AND (when this run triages credentials) the verdicts —

        // from the same cached answer, with no provider call.

                            candidates, cached, secretCtx);

        }

        }

            }

        }

        }

        try {

            // Fold credential triage into the single classification call when there

            // are candidates, so the class source is sent to the provider once.

            AiClassSuggestion aiClassSuggestion;

            } else {

            }

                    aiClassSuggestion);

            }

        }

    }

    /**

     * On a classification cache hit, supplies the credential verdicts: cached when

     * present for this signature, otherwise a one-off dedicated triage call (so a

     * class whose classification was cached without verdicts still gets scored).

     *

     * @return the cached suggestion augmented with the resolved verdicts, for re-caching

     */

    private static AiClassSuggestion serveOrTriageVerdicts(AiRuntime ai, String fqcn, String classSource,

            String contentHash, String promptSignature,

            List<PromptBuilder.CredentialCandidateRef> candidates, AiClassSuggestion cached,

            CredentialTriageContext secretCtx) {

        }

        }

        try {

            }

        }

    }

    /**

     * Returns a copy of {@code suggestion} with its credential verdicts replaced.

     *

     * @param suggestion the classification result to copy; never {@code null}

     * @param secrets    the verdicts to attach; may be {@code null}

     * @return a new suggestion carrying {@code secrets}

     */

    private static AiClassSuggestion withSecrets(AiClassSuggestion suggestion,

            List<CredentialTriageVerdict> secrets) {

    }

    /**

     * The outcome of resolving one class: the override-applied per-method lookup, and

     * the raw AI answer to persist in the cache ({@code null} when nothing should be

     * cached — no AI, no methods, oversized source, or a failed call).

     *

     * @param lookup    per-method suggestion lookup fed to the sink; never {@code null}

     * @param cacheable the full AI answer to cache, or {@code null}

     */

    }

    /**

     * The result of scanning one root: whether any provider errored, and the unified

     * cache entries collected for the classes processed in that root.

     *

     * @param hadErrors    {@code true} if any provider reported a non-fatal error

     * @param cacheEntries cache entries keyed by content hash; never {@code null}

     */

    }

}

Mutations

2.2
Location : scan
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : scan
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : scan
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

1.1
Location : scan
Killed by : none removed call to org/egothor/methodatlas/command/PluginLoader::closeAll → SURVIVED Covering tests

2.2
Location : scan
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : scan
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : runDiscoveryInternal
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

1.1
Location : processClass
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : processClass
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

3.3
Location : processClass
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

4.4
Location : processClass
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

5.5
Location : processClass
Killed by : org.egothor.methodatlas.command.ScanOrchestratorCacheTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.command.ScanOrchestratorCacheTest]/[method:cacheHit_withMatchingSignatureAndVerdicts_servesBothWithoutAnyEngineCall(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

6.6
Location : processClass
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

1.1
Location : processClass
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : processClass
Killed by : org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_contentHashIs64CharLowercaseHex_whenEnabled(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

1.1
Location : processClass
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

2.2
Location : processClass
Killed by : org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_contentHashIs64CharLowercaseHex_whenEnabled(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

1.1
Location : processClass
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : processClass
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests